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JPMML-Model: Extending PMML documents with custom XML content

Written by Villu Ruusmann on 15 May 2015

The XML data format is commonly despised for its complexity and verbosity, especially in comparison with other text-based data formats such as JSON and YAML. However, there are several application areas where its design proves to be an asset instead of a liability.

One of such application areas is extensibility. An XML document can combine different XML document types. Such mixed XML documents can be safely authored and processed using the most common XML tools and APIs.

The PMML document type is a top-level XML document type. It does not limit the number and kind of embedded XML document types. However, it is rather strict about where custom XML content can be attached to.

There are three main attachment points:

The JPMML-Model library represents attachment points as List-type fields whose element type is java.lang.Object. For example, the Extension#content field and the corresponding getter method Extension#getContent() are defined as follows:

package org.dmg.pmml;

@XmlRootElement(name = "Extension", namespace = "http://www.dmg.org/PMML-4_2")
public class Extension extends PMMLObject {

  @XmlMixed
  @XmlAnyElement(lax = true)
  private List<Object> content;


  public List<Object> getContent(){
    if(this.content == null){
      this.content = new ArrayList<Object>();
    }
    return this.content;
  }
}

The JPMML-Model library provides full support for producing and consuming mixed PMML documents.

Application developers can choose between two API approaches:

The current blog post details a method for working with PMML documents that embed MathML content. Mathematical Markup Language (MathML) is an XML-based standard for describing mathematical notations and capturing both its structure and content. It is potentially useful for adding human- and machine-readable documentation to data transformations.

The XML Schema Definition (XSD) for MathML version 3 is is readily available. It can be compiled to JAXB class model with the help of the XJC binding compiler. The generated MathML class model consists of a number of classes in the org.wc3.math package. By convention, the XML registry class is named org.w3c.math.ObjectFactory.

Production

W3C DOM approach

The MathML content is captured as an org.w3c.dom.Element object. It is critical that the W3C DOM API is operated in an XML namespace-aware fashion. This involves calling the javax.xml.parsers.DocumentBuilderFactory#setNamespaceAware(boolean) method with true as an argument and using the org.w3c.dom.Document#createElementNS(String, String) method for creating Element nodes.

private static final DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();

static {
  documentBuilderFactory.setNamespaceAware(true);
}

private org.wc3.dom.Element createMathML(){
  DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();

  Document document = documentBuilder.newDocument();

  Element element = document.createElementNS("http://www.w3.org/1998/Math/MathML", "mathml:math");
  // Create MathML content
  // All child elements should specify the same namespace URI ("http://www.w3.org/1998/Math/MathML") and namespace prefix ("mathml") as the root element

  return element;
}

The completed MathML object is then appended to the list of vendor extensions:

/**
 * Wraps a MathML object into an {@link Extension} element and appends it to the live list of extensions.
 *
 * @param hasExtensions A PMML object that supports extensions.
 * @param mathObject A MathML W3C DOM node or JAXB object.
 */
static
public void addMathML(HasExtensions hasExtensions, Object mathObject){
  List<Extension> extensions = hasExtensions.getExtensions();

  Extension extension = new Extension()
    .addContent(mathObject);

  extensions.add(extension);
}

A PMML class model object that is enriched with custom XML content in the form of W3C DOM nodes can be marshalled to a PMML document using the org.jpmml.model.JAXBUtil#marshalPMML(org.dmg.pmml.PMML, javax.xml.transform.Result) utility method.

The resulting mixed PMML document:

<?xml version="1.0" standalone="yes"?>
<PMML xmlns="http://www.dmg.org/PMML-4_2" version="4.2">
  <!-- Omitted PMML content -->
  <Extension>
    <mathml:math xmlns:mathml="http://www.w3.org/1998/Math/MathML">
      <!-- Omitted MathML content -->
    </mathml:math>
  </Extension>
</PMML>
JAXB approach

The MathML content is captured as a org.w3c.math.Math object. The JAXB class model classes are properly annotated with XML namespace information. Therefore, the application developer can focus on high-level work with POJOs.

private org.w3c.math.Math createMathML(){
  Math math = new Math();
  // Create MathML content

  return math;
}

Unlike with the W3C DOM approach, a PMML class object that is enriched with JAXB objects cannot be marshalled using the JAXBUtil#marshalPMML(PMML, Result) utility method because of the following exception:

javax.xml.bind.MarshalException - with linked exception:
[com.sun.istack.internal.SAXException2: class org.w3c.math.Math nor any of its super class is known to this context.
javax.xml.bind.JAXBException: class org.w3c.math.Math nor any of its super class is known to this context.]
  at com.sun.xml.internal.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:311)
  at com.sun.xml.internal.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:236)
  ... 3 more
Caused by: com.sun.istack.internal.SAXException2: class org.w3c.math.Math nor any of its super class is known to this context.
javax.xml.bind.JAXBException: class org.w3c.math.Math nor any of its super class is known to this context.
  at com.sun.xml.internal.bind.v2.runtime.XMLSerializer.reportError(XMLSerializer.java:235)
  at com.sun.xml.internal.bind.v2.runtime.XMLSerializer.reportError(XMLSerializer.java:250)
  at com.sun.xml.internal.bind.v2.runtime.property.ArrayReferenceNodeProperty.serializeListBody(ArrayReferenceNodeProperty.java:107)
  ... 28 more
Caused by: javax.xml.bind.JAXBException: class org.w3c.math.Math nor any of its super class is known to this context.
  at com.sun.xml.internal.bind.v2.runtime.JAXBContextImpl.getBeanInfo(JAXBContextImpl.java:564)
  at com.sun.xml.internal.bind.v2.runtime.property.ArrayReferenceNodeProperty.serializeListBody(ArrayReferenceNodeProperty.java:97)
  ... 28 more

Just like the exception message suggests, the solution is to make the MathML class model known to the JAXB runtime.

A javax.xml.bind.JAXBContext instance can be created by calling the JAXBContext#newInstance(Class...) method with a list of XML registry classes as arguments. Currently, this list must include org.dmg.pmml.ObjectFactory and org.w3c.math.ObjectFactory classes.

A custom JAXBContext instance passes complete type information to its child javax.xml.bind.Marshaller and javax.xml.bind.Unmarshaller instances. The marshalling and unmarshalling behaviour can be further modified by adjusting generic as well as implementation-specific configuration options. For example, setting the generic jaxb.formatted.output configuration option to true will indentate the XML document to make it more human friendly:

private static JAXBContext mixedContext = null;

static
private JAXBContext getOrCreateMixedContext() throws JAXBException {

  if(mixedContext == null){
    mixedContext = JAXBContext.newInstance(org.dmg.pmml.ObjectFactory.class, org.w3c.math.ObjectFactory.class);
  }

  return mixedContext;
}

static
public Marshaller createMixedMarshaller() throws JAXBException {
  JAXBContext context = getOrCreateMixedContext();

  Marshaller marshaller = context.createMarshaller();
  marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, Boolean.TRUE);

  return marshaller;
}

static
public Unmarshaller createMixedUnmarshaller() throws JAXBException {
  JAXBContext context = getOrCreateMixedContext();

  Unmarshaller unmarshaller = context.createUnmarshaller();

  return unmarshaller;
}

The resulting mixed PMML document:

<?xml version="1.0" standalone="yes" ?>
<PMML xmlns="http://www.dmg.org/PMML-4_2" xmlns:ns2="http://www.w3.org/1998/Math/MathML" version="4.2">
  <!-- Omitted PMML content -->
  <Extension>
    <ns2:math>
      <!-- Omitted MathML content -->
    </ns2:math>
  </Extension>
</PMML>

Consumption

The "completeness" of unmarshalling operation depends on which JAXB class models are known to the JAXB runtime. In brief, known XML content is returned in the form of JAXB objects, whereas unknown XML content is returned in the form of W3C DOM nodes.

The JAXBUtil#unmarshalPMML(javax.xml.transform.Source) utility method is only aware of the PMML class model. Therefore, all custom XML content is returned in the form of W3C DOM nodes. In that sense, JAXBUtil#marshalPMML(PMML, Result) and JAXBUtil#unmarshal(Source) utility methods are reciprocal to one another.

Sometimes it may be desirable to defer the unmarshalling of custom XML content. For example, the PMML content is unmarshalled completely during the first pass, whereas MathML content is unmarshalled either completely or on an XML node basis (eg. rendering a tooltip) during subsequent passes.

The following code replaces MathML W3C DOM nodes with the corresponding JAXB objects:

private static JAXBContext mathMlContext = null;

static
private JAXBContext getOrCreateMathMLContext() throws JAXBException {

  if(mathMlContext == null){
    mathMlContext = JAXBContext.newInstance(org.w3c.math.ObjectFactory.class);
  }

  return mathMlContext;
}

/**
 * @param hasExtensions A PMML object that supports extensions.
 */
static
public void unmarshalMathML(HasExtensions hasExtensions) throws JAXBException {
  JAXBContext context = getOrCreateMathMLContext();

  Unmarshaller unmarshaller = context.createUnmarshaller();

  List<Extension> extensions = hasExtensions.getExtensions();
  for(Extension extension : extensions){
    List<Object> content = extension.getContent();

    for(int i = 0; i < content.size(); i++){
      Object object = content.get(i);

      if(object instanceof org.w3c.dom.Element){
        org.w3c.dom.Element element = (org.w3c.dom.Element)object;
        org.w3c.math.Math math = (org.w3c.math.Math)unmarshaller.unmarshal(new DOMSource(element));

        content.set(i, math);
      }
    }
  }
}
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